The Awakening
by AskEmily94
Summary: Thomas falls asleep beside the Gladers after being rescued from the Safe Haven, but when he awakes he is not in the Berg. Instead he is shocked to find that he has awoken in the maze again, beside his friends that have died. With only his closest friends that remember, Thomas is on a mission to discover what is reality and attempts to stop the group from ever leaving the maze.
1. Chapter 1

_Notes: This is my first maze runner fan fiction, I've only read the first two books but I immediately fell in love with the characters! I got the third book today which I will be reading soon, but I was trying to guess what was going to happen and started to wonder if they ever actually got out of the maze at all, which is where this little plot bunny came from. This is based exactly just after the end of The Scorch Trials books so beware of spoilers. I kind of ship Thomas/Newt and Thomas/Minho, but I don't know if I will ever even write romance In this or not. Anyway, I hope you guys enjoy the story! Let me know what you think in the comments below!_

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Thomas lay on the couch in the Berg, body sore from days of traveling the Scorch and fighting. Thomas knew this could be just like the dormitory all over again, that they could possibly be lured into a false sense of security just to have it ripped away all over again, but as he lay there listening to the soft murmurs of the Gladers conversations he felt his eyelids begin to droop, and despite his wariness, he quickly drifted off to sleep.

"Thomas, Wake up!" It was Minho's voice, barely noticeable through his sleepy haze. Thomas shifted and stirred, longing for a few more moments of peaceful oblivion. "Thomas, wake up you shuckhead!" He groaned in protest and put his arm over his eyes to block them from the sunlight shining from above. Wait a minute, sunlight? Thomas was immediately awake. Why was there sunlight, the last he remembered he was in the Berg?

He was greeted with both Minho's and Newt's concerned faces. Thomas began to ask what was wrong when he noticed where he was; he was in the Glade.

Thomas bolted upright, stomach doing summersaults. No, he couldn't possibly be back in the glade could he? This had to be a dream, a horrible, completely made up dream. In fact, he was probably sleeping beside the Gladers in the Berg right now. But as he took in a few Gladers sleeping beside him that hadn't yet woken up, the sweet smell of trees, and the feeling of the soft, spongy, grass underneath him, Thomas began to doubt this was just an ordinary dream.

"Are we-?"

"We are back in the glade," Newt answered his silent question grimly.

"But how-" Thomas's question trailed off as he remembered the words of the scientist back in the dorm.

 **"If I can tell you anything today it is that you should never, ever believe your eyes. Or your mind for that matter. All I will say is that sometimes what you see is not real, and sometimes what you do not see is real."**

Thomas shivered despite the warm air and felt a deep sense of foreboding.

"Do you remember what the scientist said that day in the dormitory? About some stuff not being real? What if all of this stuff we've been through, the whole thing, was all in our heads?" Thomas asked.

Newt nodded grimly. "I've been wondering the same thing. But it all felt so real, and what about people dying? And being hurt? I don't see how any of that could possibly be fake."

"But what about those dead bodies that were hanging from the ceiling in the dormitories?" Minho argued. "We could feel ourselves bumping into them, and could smell the stench coming off of them, and they weren't even there. But maybe Newt is right, maybe all of that was real and this is fake. But I don't see how we could possibly begin to find out which is which."

Thomas ran his hand through his hair in frustration and looked more closely at the Gladers beside him and the ones going about there chores around the farm. He froze as he noticed a few that he hadn't seen in a long time. "Those Gladers are dead." He pointed to a few. "They died during the fight with the grievers, and I haven't seen him since the lightning storm."

Minho nodded. "We noticed, Newt woke me up just a minute ago after he realized where we were."

"Have you tried talking to any of them?" Thomas questioned.

"What do you take me for, a Shank? I told you we just woke up a minute ago. We figured we would wake you up before we did anything. I don't see Frypan anywhere but from what it looks like, it doesn't seem like anybody else remembers anything. They are all going about their chores like we never left."

Thomas exhaled deeply and ran a hand through his hair frustrated. "I can't believe this. What are we supposed to do?"

An alarm started blaring and everybody stopped in their tracks. It was the alarm to announce a new arrival. Thomas'a heart skipped a beat and in a silent agreement, they nodded and ran towards the box.


	2. Chapter 2

_Notes: Omg, I just finished reading The Death Cure and I think I may need therapy...(Spoiler Alert) I can't believe they killed Newt! I cried for a few hours and then decided that I am totally going to forget the last book ever happened. All along it was just happening in their head...yeah..all in their head... ANYWAY, in this story there is probably going to be a lot of different stuff than the original story, just because it would be boring to read everything exactly the same all over again, and I may also leave out a character or too for the same reasons. Anyway, I hope you enjoy this chapter!_

Newt, Thomas, and Minho ran to the box where all of the Gladers were gathering. Newt stopped in his tracks as he saw Alby, and Thomas put a hand on his shoulder in an attempt to comfort him. Hesitantly Newt stepped forward and pried the box open alongside Alby. Everybody fell silent and Thomas held his breath waiting for confirmation to his suspicions.

"No way," Alby muttered.

Everybody began asking questions at once and pushed forward to try and get a better look. Thomas was struck with a severe case of dejavu.

Alby stood up. "Two Newbies in two days. He said quietly. "Now this. Two years, nothing different, now this." Then he looked at Thomas. "What's going on here Greenie?"

Thomas felt his chest tighten, looking at the boy. The only thing he could think of was of that horrible moment when the Grievers tore his body apart, with nothing they could do but watch in silent horror. Thomas looked at Newt.

"We need to call a gathering. Now."

As the group of Gladers pulled Teresa out and called over the medjacks, Minho pulled Newt and Thomas off to the side where they could speak without the ruckus.

"What do you think is going on here? Most of these people are supposed to be dead! Do you think we somehow got sent back to the past or something?" Thomas questioned rapidly.

Minho shook his head. "Those Shuck scientists can do a lot but their technology isn't quite that advanced."

Newt nodded in agreement with Minho. "No, I think it's a matter of illusion. Either all the stuff and the trials we went through was an illusion or this is."

"But how can we tell the difference?" Questioned Thomas. "It all feels so real. And why would Wicked put us through that as an illusion and then do it all over again in real life?"

Newt shook his head. "I'm just as stumped as you are, Tommy. Maybe Wicked made us think we were going through all of that, as an illusion, just to make sure it would all go as they planned?"

"That doesn't make a shuck of sense. If we knew all the horrible stuff that was going to happen if we made those decisions, then we are obviously going to do the opposite," Minho denied.

"Then maybe thats what they were testing." Thomas suggested. "Maybe it didn't look like it was going to go as planned, so they made us think we had gone through all that so they could see what would happen and how to do it and control us better the second time. Or maybe they wanted to make sure not too many of us died, and this is how we could potentially save some of us? By doing it all over a second time with more knowledge."

Minho ran a hand through his hair, frustrated. "Well, I don't know about you guys but my brain hurts just trying to figure this all out. What we really need to decide is what we are going to do. We can't just wait and see what happens just because there is a chance that this is an illusion."

Newt nodded slowly. "You're right. We have no way of knowing if this is real or not and standing around guessing isn't going to help. This might be real, and those kids might be real, so illusion or not, we need to try and save them and act as if this is life or death, even if it isn't."

They all agreed. "But what are we all going to do next? Do we tell them? Should we even try to leave the maze?" Thomas asked with a furrowed brow.

"What do you mean?" Newt asked.

"Call me crazy, but I'm just thinking we might stand a better chance if we stay. If things go like we remember, then eventually the sun will disappear and the gates won't close, but just trying to escape the maze, and out there in the scorch, more of us probably died then than if we had stayed,"Explained Thomas.

"I've always hated this shuck maze, but you may be right. Nearly all of us died out there. If things are the same, then no matter how hard we try, some will most likely die here, but I think the odds are more in our favor if we stay,"Newt agreed.

"I'm all for that plan,"Minho said. "But soon our supplies and food are going to stop coming, and the plants are going to die. Then we won't have anything to eat."

"True, but if Frypan is around here somewhere we can tell him to be careful with our supplies and it will still take awhile for the plants to die. If anything it will give us time to explain everything that happened to the others and come up with a plan. I don't think the others would believe me, after all it seems like I've only been here for a day, but everybody trusts you two. If you can convince them that we are telling the truth, then I'm sure we can start trying to board up the homestead right away against the Grievers." Thomas said.

"Good that." Agreed Minho. "Okay, Newt, you go find Alby and convince him to have a gathering. I'll go get Zart and Winston. Thomas, you go try and find Frypan. See if he is around here somewhere and if he remembers us. We will all gather at the homestead in ten or so minutes."

They all agreed and began collecting people for the gathering.


	3. Chapter 3

_Notes: So this Chapter was actually quite difficult to write. Its not my best work, after all, it is quite hard to write someone explain something so far fetched and have the others believe them. Alas, I hope you guys enjoy it anyway. Comments and suggestions are always welcome! If you have any ideas on what to do next for the story or anything you want to see, let me know and I might just make it happen! :)_

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Thomas, Minho, Newt, Winston, Zart, Alby, and Frypan all sat in the homestead in a circle around the table. Thomas had found Frypan looking around the glade, trying to figure out what was going on just like them. Apparently Frypan could remember, but Frypan had spoken to one of the Gladers that had survived with them and the Glader had no memory of anything.

'But why would only the three of us have any memory of what happened?' Thomas wondered.

"So are you going to tell us what I called this bloody gathering for and why the Greenie is here, or are we going to continue sitting in silence for the remainder of the day?" Alby asked, annoyed.

All eyes turned to Newt and he took a deep breath to calm his nerves.

"Okay, I know this is going to sound crazy, but all of this happened weeks ago."

"What was weeks ago?" Zart questioned.

"All of this," Newt answered seriously. "What I mean is, we have been through all of this before, that girl has shown up here before, Thomas arrived here weeks ago. I know it doesn't make any sense, but a few weeks ago weird things started happening here at the glade. The girl arrived and a few days later the sun suddenly disappeared. Then later the supplies we were supposed to get as usual, didn't come. Then one day, the doors to the maze didn't close. We boarded up the homestead and stayed in there while we tried to figure out a plan. Thomas got stung and went through the changing where he remembered that he used to be forced to work for the creators. They made him help build the maze and going through the changing made him remember how to get out. The way out is the cliff, there is a hole in the middle of it that you jump through. Inside there is a room with a computer, we figured out the code to enter into the computer to shut down the grievers. We all gathered together with weapons and tried to fend off the grievers while Thomas and Teresa, the girl, could enter the code but many of us died. Outside the world is in chaos! It ain't anything like we remember. Years ago there was this thing people called the flare. It burnt half the world and somehow unleashed a virus that makes people go crazy and violent, they call the infected people cranks. There are cranks all over the world and very few well people. The creators that built this maze and put us in here are making us go through these trials, they make us do things and they say somehow in the end it will help them find a cure. They made us travel through the scorch, a huge area of burnt land. By the time we got where we were supposed to go, only a few of us had survived. They picked us up in this thing called a Berg, and we fell asleep, but when we woke up, we were back in the maze again this morning, and only Thomas, Minho, and I remember anything!" Newt explained rapidly.

There was silence for a moment where everybody looked at the three of them, almost as if waiting for the punch like to some kind of sick joke, but it never came.

"That sounds like a pile of klunk. Even if what you are saying is true, if this all happened weeks ago and we somehow got our minds wiped or something, then why are we all still alive? You said nearly all of us were dead, but if you haven't noticed, we are all alive and kicking,"Alby pointed out.

"Obviously,"said Minho, coming to Newts defense. "That's why we are so confused and shocked. The thing is, when we got out of the maze, the creators took us to this bunker for a night. When we woke up in the morning and came out of our room, we realized there were a ton of dead bodies strung up by their necks. We bumped into them, could feel and smell them, but when we came back just a few minutes later, they were gone. It was all an illusion. One of the creators said that we should never trust our eyes because what we are seeing may not be real, so there is a possibility that the whole thing was fake, an illusion. But there is also a chance that this is the thing that's fake. We don't know, but what we do know is things are happening all over again. Teresa arrived today which means soon the sun will disappear, and that everything else will happen soon. We need to come up with a plan."

"I know how crazy it sounds, and I know that all any of us have ever wanted was to get out of this shuck maze, but out there is horrible. Nearly all of us will die, we have to find another way. I can't see all of you die again, I can't,"Newt said, and Thomas was shocked to see tears in his friends eyes.

Apparently Alby realized that his friend was serious, as well as Zart and Winston.

"Okay, I believe you,"Alby said tentatively, and it felt as if a giant weight had been taken off of Newt's shoulders.

Alby took a deep breath. "Why don't you start from the beginning. Explain everything that happened, and I mean _everything_. If we are going to do things different the second time around and make a plan, we need to know what happened, who died, where we went, and more about these creators."

Everybody nodded, apparently agreeing, and Thomas felt a surge of gratitude from how quickly their friends would believe something so impossible, just because they swore it to be true.

Thomas sat back and made himself comfortable as Newt began to speak. They were going to be here for awhile.


End file.
